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https://github.com/bids-apps/SPM
BIDS App containing an instance of the SPM software.
https://github.com/bids-apps/SPM
bids bidsapp spm
Last synced: about 2 months ago
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BIDS App containing an instance of the SPM software.
- Host: GitHub
- URL: https://github.com/bids-apps/SPM
- Owner: bids-apps
- License: apache-2.0
- Created: 2016-08-02T15:47:06.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2024-04-30T09:47:16.000Z (5 months ago)
- Last Synced: 2024-06-21T07:22:16.499Z (3 months ago)
- Topics: bids, bidsapp, spm
- Language: MATLAB
- Homepage: https://hub.docker.com/r/bids/spm/tags
- Size: 77.1 KB
- Stars: 14
- Watchers: 8
- Forks: 11
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-bids - SPM
README
# SPM BIDS App
## Description
[BIDS App](http://bids-apps.neuroimaging.io/) containing an instance of the [SPM12 software](http://www.fil.ion.ucl.ac.uk/spm/).
## Documentation
Extensive documentation can be found in the [SPM manual](http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf).
## Usage
To launch an instance of the container and analyse some data in BIDS format, type:
```bash
$ docker run bids/spm bids_dir output_dir level [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--config CFG_FILE]
```
For example, to run an analysis in ```participant``` level mode, type:
```bash
$ docker run -ti --rm \
-v /tmp:/tmp \
-v /var/tmp:/var/tmp \
-v /path/to/local/bids/input/dataset/:/data \
-v /path/to/local/output/:/output \
bids/spm \
/data /output participant --participant_label 01
```
For example, to run an analysis in ```group``` level mode with a user-defined pipeline, type:
```bash
$ docker run -ti --rm \
-v /tmp:/tmp \
-v /var/tmp:/var/tmp \
-v /path/to/local/bids/input/dataset/:/data \
-v /path/to/local/output/:/output \
-v /path/to/local/cfg/:/cfg \
bids/spm \
/data /output group --config /cfg/my_pipeline_group.m
```
To build the container, type:
```bash
$ docker build -t /spm12 .
```
### Configuration file
The configuration file is a MATLAB script detailing the analysis pipeline to be executed. Two struct variables, ```BIDS``` and ```BIDS_App``` are available from within the script, containing details from the command line and the BIDS-formatted dataset. In particular, the ```BIDS``` structure can be queried using the ```spm_BIDS()``` function (see [this](https://en.wikibooks.org/wiki/SPM/BIDS)). The default configuration files for first and second level analyses are ```pipeline_participant.m``` and ```pipeline_group.m```. A template for a single configuration file for all levels could be as follow:
```bash
if strcmp(BIDS_App.level,'participant')
% First level analysis
% Get T1-weighted image filename for given subject:
% a = spm_BIDS(BIDS,'data', 'modality','anat', 'type','T1w');
% ...
else
% Second level analysis
% The name of the directory containing first level outputs is stored in:
% BIDS_App.outdir
% ...
end
```
## Error Reporting
If you have a specific problem with the SPM BIDS App, please open an [issue](https://github.com/BIDS-Apps/SPM/issues) on GitHub.
If your issue concerns SPM more generally, please use the [SPM mailing list](https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=spm).
## Acknowledgement
Please refer to:
```
@Book{spm,
editor = {K.J. Friston and J. Ashburner and S.J. Kiebel and T.E. Nichols and W.D. Penny},
title = {Statistical Parametric Mapping: The Analysis of Functional Brain Images},
publisher = {Academic Press},
year = {2007},
url = {http://store.elsevier.com/product.jsp?isbn=9780123725608}
}
```